SMTL ID : 6nt1.1

Catalase 3 from N.Crassa in ferrous state (2.89 MGy)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 27 residues within 4Å: Chain A: R.99, V.100, V.101, H.102, R.139, G.158, F.159, A.160, V.173, G.174, N.175, F.180, A.185, F.188, I.248, H.249, F.365, L.381, G.384, R.385, S.388, Y.389, T.392, Q.393, R.396 Chain D: L.88, D.92 32 PLIP interactions: 31 interactions with chain A, 1 interactions with chain D, Hydrophobic interactions: A:V.100, A:H.102, A:A.160, A:V.173, A:F.180, A:F.180, A:A.185, A:F.188, A:F.188, A:F.188, A:F.188, A:I.248, A:I.248, A:F.365, A:L.381, A:L.381, A:R.385, A:Y.389, A:Y.389, D:L.88 Hydrogen bonds: A:R.139, A:Q.393 Water bridges: A:V.100, A:T.392 Salt bridges: A:R.99, A:R.99, A:R.139, A:R.396 pi-Stacking: A:H.102, A:F.188 pi-Cation interactions: A:R.385 Metal complexes: A:Y.389 HEM.9: 27 residues within 4Å: Chain B: R.99, V.100, V.101, H.102, R.139, G.158, F.159, A.160, V.173, G.174, N.175, F.180, A.185, F.188, I.248, H.249, F.365, L.381, G.384, R.385, S.388, Y.389, T.392, Q.393, R.396 Chain C: L.88, D.92 35 PLIP interactions: 34 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:V.100, B:H.102, B:A.160, B:V.173, B:N.175, B:F.180, B:F.180, B:A.185, B:F.188, B:F.188, B:F.188, B:F.188, B:I.248, B:I.248, B:F.365, B:L.381, B:L.381, B:R.385, B:Y.389, B:Y.389, B:T.392, C:L.88 Hydrogen bonds: B:Q.393 Water bridges: B:V.100, B:R.139, B:A.160, B:T.392 Salt bridges: B:R.99, B:R.99, B:R.139, B:R.396 pi-Stacking: B:H.102, B:F.188 pi-Cation interactions: B:R.385 Metal complexes: B:Y.389 HEM.18: 26 residues within 4Å: Chain B: L.88, D.92 Chain C: R.99, V.100, V.101, H.102, R.139, G.158, F.159, V.173, G.174, N.175, F.180, A.185, F.188, I.248, H.249, F.365, L.381, G.384, R.385, S.388, Y.389, T.392, Q.393, R.396 31 PLIP interactions: 29 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: C:V.100, C:V.101, C:H.102, C:V.173, C:F.180, C:F.180, C:A.185, C:F.188, C:F.188, C:F.188, C:F.188, C:F.365, C:L.381, C:L.381, C:R.385, C:Y.389, B:L.88 Hydrogen bonds: C:Q.393 Water bridges: C:R.139, C:A.160, C:T.392, C:T.392 Salt bridges: C:R.99, C:R.99, C:R.139, C:R.396 pi-Stacking: C:H.102, C:F.188 pi-Cation interactions: C:R.385 Metal complexes: C:Y.389, H2O.52 HEM.29: 26 residues within 4Å: Chain A: L.88 Chain D: R.99, V.100, V.101, H.102, R.139, G.158, F.159, A.160, V.173, G.174, N.175, F.180, A.185, F.188, I.248, H.249, F.365, L.381, G.384, R.385, S.388, Y.389, T.392, Q.393, R.396 34 PLIP interactions: 32 interactions with chain D, 1 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: D:V.100, D:V.101, D:H.102, D:A.160, D:V.173, D:F.180, D:F.180, D:A.185, D:F.188, D:F.188, D:F.188, D:F.188, D:I.248, D:I.248, D:F.365, D:L.381, D:L.381, D:R.385, D:Y.389, D:Y.389, A:L.88 Hydrogen bonds: D:Q.393 Water bridges: D:V.100, D:R.139, D:T.392 Salt bridges: D:R.99, D:R.99, D:R.139, D:R.396 pi-Stacking: D:H.102, D:F.188 pi-Cation interactions: D:R.385 Metal complexes: D:Y.389, H2O.70

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 7 residues within 4Å: Chain A: V.143, A.144, D.155, V.156, F.181, I.192, V.195 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.143, A:F.181, A:I.192, A:V.195 Hydrogen bonds: A:V.156 Water bridges: A:D.155, A:D.155 ACT.3: 8 residues within 4Å: Chain A: N.176, N.234, P.237, H.242, M.243, K.273, A.274, I.558 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.237, A:I.558 Hydrogen bonds: A:N.176, A:D.244 Water bridges: A:N.234, A:N.234 ACT.10: 7 residues within 4Å: Chain B: V.143, A.144, D.155, V.156, F.181, I.192, V.195 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.143, B:F.181, B:I.192, B:V.195 Water bridges: B:V.156, B:V.156 ACT.11: 8 residues within 4Å: Chain B: N.176, N.234, P.237, H.242, M.243, K.273, A.274, I.558 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.237, B:I.558 Hydrogen bonds: B:N.176 Water bridges: B:N.234, B:N.234, B:D.244 ACT.19: 7 residues within 4Å: Chain C: V.143, A.144, D.155, V.156, F.181, I.192, V.195 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.143, C:F.181, C:I.192, C:V.195 Hydrogen bonds: C:V.156 ACT.20: 9 residues within 4Å: Chain C: N.176, N.234, P.237, H.242, M.243, D.244, K.273, A.274, I.558 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:P.237, C:I.558 Hydrogen bonds: C:N.176, C:N.234, C:D.244 Water bridges: C:N.234 ACT.30: 6 residues within 4Å: Chain D: V.143, A.144, D.155, V.156, F.181, V.195 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.143, D:F.181, D:V.195 Hydrogen bonds: D:V.156 ACT.31: 8 residues within 4Å: Chain D: N.176, N.234, P.237, H.242, M.243, K.273, A.274, I.558 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:P.237, D:I.558 Hydrogen bonds: D:N.176, D:N.234 Water bridges: D:N.234, D:N.234, D:D.244, D:D.244

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 4 residues within 4Å: Chain A: T.600, Q.612, A.616, A.621 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.612, A:D.618 Water bridges: A:K.287, A:N.288, A:A.616, A:A.617, A:T.620 PGE.12: 3 residues within 4Å: Chain B: T.600, Q.612, A.621 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.288, B:K.598, B:Q.612 PGE.23: 2 residues within 4Å: Chain C: S.488, V.552 No protein-ligand interaction detected (PLIP) PGE.32: 6 residues within 4Å: Chain A: S.651, Q.652, T.655, R.659 Chain D: Q.652, R.659 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:T.655, D:R.659, D:R.659, A:R.659

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 2 residues within 4Å: Chain A: D.477, Y.547 No protein-ligand interaction detected (PLIP) PEG.6: 3 residues within 4Å: Chain A: Y.438, L.439, K.441 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.441 Water bridges: A:K.441 PEG.13: 6 residues within 4Å: Chain B: T.655, Y.658, R.659, I.677, V.679 Ligands: P6G.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.659 PEG.24: 2 residues within 4Å: Chain C: Y.323, G.324 1 PLIP interactions: 1 interactions with chain C Water bridges: C:G.324 PEG.25: 4 residues within 4Å: Chain C: R.570, T.600, D.611, Q.612 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.570 Water bridges: C:R.570, C:K.598, C:K.598

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 6 residues within 4Å: Chain A: P.335, E.337, F.338, L.484, N.551, V.552 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.337, A:V.552 Water bridges: A:N.551 EDO.14: 3 residues within 4Å: Chain B: Y.438, L.439, K.441 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.441 Water bridges: A:N.510 EDO.15: 4 residues within 4Å: Chain B: F.338, L.484, N.551, V.552 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.551 Water bridges: B:H.549 EDO.26: 4 residues within 4Å: Chain C: R.409, G.413, V.414, W.426 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.409, C:V.414, C:V.414 EDO.27: 4 residues within 4Å: Chain C: S.198, D.200, N.201 Chain D: I.431 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.198, C:S.198, C:N.201 EDO.28: 2 residues within 4Å: Chain C: T.546, Y.547 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.477 EDO.33: 3 residues within 4Å: Chain D: Y.438, L.439, K.441 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.438, D:K.441 EDO.34: 3 residues within 4Å: Chain D: Q.321, F.325, T.474 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:F.325 Water bridges: D:G.324 EDO.35: 4 residues within 4Å: Chain D: T.480, H.549, N.551 Ligands: EOH.37 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.549, D:N.551

6 x EOH: ETHANOL(Non-functional Binders)

EOH.8: 2 residues within 4Å: Chain A: E.317, G.460 No protein-ligand interaction detected (PLIP) EOH.16: 3 residues within 4Å: Chain B: E.317, G.460, R.461 No protein-ligand interaction detected (PLIP) EOH.17: 2 residues within 4Å: Chain B: L.708, E.709 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.708 EOH.36: 4 residues within 4Å: Chain B: E.45, V.48 Chain D: R.409, W.426 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.409, D:R.409 EOH.37: 4 residues within 4Å: Chain D: E.337, F.338, V.552 Ligands: EDO.35 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.338 Hydrogen bonds: D:V.552 EOH.38: 3 residues within 4Å: Chain D: R.659, I.677, G.678 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.659

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.21: 12 residues within 4Å: Chain B: A.640, S.651, Q.652, T.655, R.659 Chain C: A.640, G.648, S.651, Q.652, T.655, R.659 Ligands: PEG.13 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:G.648, C:S.651, C:R.659, C:R.659, B:S.651, B:R.659

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.22: 6 residues within 4Å: Chain C: W.118, I.121, L.341, Q.342, V.343, L.344 2 PLIP interactions: 2 interactions with chain C Water bridges: C:L.341, C:V.343

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zarate-Romero, A. et al., X-ray driven reduction of Cpd I of Catalase-3 from N. crassa reveals differential sensitivity of active sites and formation of ferrous state. Arch.Biochem.Biophys. (2019)

Release Date

2019-05-01

Peptides

Catalase-3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Catalase-3

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